[gmx-users] amber DNA non-integer charge
Kamesh Narasimhan
g0701207 at nus.edu.sg
Mon Aug 29 08:02:19 CEST 2011
Yes, you were right, upgrading it to 4.5.4 made sure the atom types/charges in the DNA termini were recognized correctly. This time the topology got generated with integer charges.
thanks
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Monday, August 29, 2011 3:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] amber DNA non-integer charge
Kamesh Narasimhan wrote:
> I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are as you mentioned.
>
> "H1 amber99_17 0.35200 19"
>
> But in my top file the H1 atom of the type amber99_17 gets replaced by the amber99_25 type
>
> so what should have been
>
> amber99_17 1 DG5 H1 19 0.35200 1.008 ;
>
> is written by pdb2gmx as
>
> amber99_25 1 DG5 H1 19 0.4422 1.008 ;
>
> How can I make amber generate the topology with the right atomtype and charge in this case?. Thanks in advance.
>
I don't know, but it's not productive to troubleshoot buggy behavior in a
Gromacs version that is over two years old. I'd suggest upgrading to the newest
version (4.5.4, with the appropriate version of the Amber ports) and seeing if
the behavior persists. Otherwise, edit the topology manually to correct the error.
-Justin
> my top file:
>
> 1 amber99_43 1 DG5 O5' 1 -0.6318 16 ; qtot -0.6318
> 2 amber99_25 1 DG5 H5T 2 0.4422 1.008 ; qtot -0.1896
> 3 amber99_11 1 DG5 C5' 3 -0.0069 12.01 ; qtot -0.1965
> 4 amber99_19 1 DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211
> 5 amber99_19 1 DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457
> 6 amber99_11 1 DG5 C4' 6 0.1629 12.01 ; qtot 0.1172
> 7 amber99_19 1 DG5 H4' 7 0.1176 1.008 ; qtot 0.2348
> 8 amber99_44 1 DG5 O4' 8 -0.3691 16 ; qtot -0.1343
> 9 amber99_11 1 DG5 C1' 9 0.0358 12.01 ; qtot -0.0985
> 10 amber99_20 1 DG5 H1' 10 0.1746 1.008 ; qtot 0.0761
> 11 amber99_40 1 DG5 N9 11 0.0577 14.01 ; qtot 0.1338
> 12 amber99_6 1 DG5 C8 12 0.0736 12.01 ; qtot 0.2074
> 13 amber99_24 1 DG5 H8 13 0.1997 1.008 ; qtot 0.4071
> 14 amber99_36 1 DG5 N7 14 -0.5725 14.01 ; qtot -0.1654
> 15 amber99_4 1 DG5 C5 15 0.1991 12.01 ; qtot 0.0337
> 16 amber99_2 1 DG5 C6 16 0.4918 12.01 ; qtot 0.5255
> 17 amber99_41 1 DG5 O6 17 -0.5699 16 ; qtot -0.0444
> 18 amber99_35 1 DG5 N1 18 -0.5053 14.01 ; qtot -0.5497
> 19 amber99_25 1 DG5 H1 19 0.4422 1.008 ; qtot -0.1075
> 20 amber99_3 1 DG5 C2 20 0.7432 12.01 ; qtot 0.6357
> 21 amber99_38 1 DG5 N2 21 -0.923 14.01 ; qtot -0.2873
> 22 amber99_17 1 DG5 H21 22 0.4235 1.008 ; qtot 0.1362
> 23 amber99_17 1 DG5 H22 23 0.4235 1.008 ; qtot 0.5597
> 24 amber99_37 1 DG5 N3 24 -0.6636 14.01 ; qtot -0.1039
> 25 amber99_4 1 DG5 C4 25 0.1814 12.01 ; qtot 0.0775
> 26 amber99_11 1 DG5 C3' 26 0.0713 12.01 ; qtot 0.1488
> 27 amber99_19 1 DG5 H3' 27 0.0985 1.008 ; qtot 0.2473
> 28 amber99_11 1 DG5 C2' 28 -0.0854 12.01 ; qtot 0.1619
> 29 amber99_18 1 DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337
> 30 amber99_18 1 DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055
> 31 amber99_44 1 DG5 O3' 31 -0.5232 16 ; qtot -0.2177
> .....
> .......
> .....
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Monday, August 29, 2011 2:41 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] amber DNA non-integer charge
>
> Kamesh Narasimhan wrote:
>> Hil,
>>
>> I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction
>>
>> "However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen".
>>
>> I replaced the aminoacids.dat contents with aminoacids-NA.dat contents and therefore not sure how the non-integer originates.
>>
>> In my top file I can see this residue of the type "amber99_25" . How do I correct for the atom-type and charge in this case ?
>>
>> " amber99_25 1 DG5 H5T 2 0.4422 1.008 ; qtot -0.1896"
>>
>>
>> My top file section:
>>
>> nr type resnr residue atom cgnr charge mass typeB chargeB massB
>> 1 amber99_43 1 DG5 O5' 1 -0.6318 16 ; qtot -0.6318
>> 2 amber99_25 1 DG5 H5T 2 0.4422 1.008 ; qtot -0.1896
>> 3 amber99_11 1 DG5 C5' 3 -0.0069 12.01 ; qtot -0.1965
>> 4 amber99_19 1 DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211
>> 5 amber99_19 1 DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457
>> 6 amber99_11 1 DG5 C4' 6 0.1629 12.01 ; qtot 0.1172
>> 7 amber99_19 1 DG5 H4' 7 0.1176 1.008 ; qtot 0.2348
>> 8 amber99_44 1 DG5 O4' 8 -0.3691 16 ; qtot -0.1343
>> 9 amber99_11 1 DG5 C1' 9 0.0358 12.01 ; qtot -0.0985
>> 10 amber99_20 1 DG5 H1' 10 0.1746 1.008 ; qtot 0.0761
>> 11 amber99_40 1 DG5 N9 11 0.0577 14.01 ; qtot 0.1338
>> 12 amber99_6 1 DG5 C8 12 0.0736 12.01 ; qtot 0.2074
>> 13 amber99_24 1 DG5 H8 13 0.1997 1.008 ; qtot 0.4071
>> 14 amber99_36 1 DG5 N7 14 -0.5725 14.01 ; qtot -0.1654
>> 15 amber99_4 1 DG5 C5 15 0.1991 12.01 ; qtot 0.0337
>> 16 amber99_2 1 DG5 C6 16 0.4918 12.01 ; qtot 0.5255
>> 17 amber99_41 1 DG5 O6 17 -0.5699 16 ; qtot -0.0444
>> 18 amber99_35 1 DG5 N1 18 -0.5053 14.01 ; qtot -0.5497
>> 19 amber99_25 1 DG5 H1 19 0.4422 1.008 ; qtot -0.1075
>
> The charge on H1 is wrong. According to the DG5 .rtp entry (in the version
> 4.5.x series), the charge should be 0.352.
>
> -Justin
>
>> 20 amber99_3 1 DG5 C2 20 0.7432 12.01 ; qtot 0.6357
>> 21 amber99_38 1 DG5 N2 21 -0.923 14.01 ; qtot -0.2873
>> 22 amber99_17 1 DG5 H21 22 0.4235 1.008 ; qtot 0.1362
>> 23 amber99_17 1 DG5 H22 23 0.4235 1.008 ; qtot 0.5597
>> 24 amber99_37 1 DG5 N3 24 -0.6636 14.01 ; qtot -0.1039
>> 25 amber99_4 1 DG5 C4 25 0.1814 12.01 ; qtot 0.0775
>> 26 amber99_11 1 DG5 C3' 26 0.0713 12.01 ; qtot 0.1488
>> 27 amber99_19 1 DG5 H3' 27 0.0985 1.008 ; qtot 0.2473
>> 28 amber99_11 1 DG5 C2' 28 -0.0854 12.01 ; qtot 0.1619
>> 29 amber99_18 1 DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337
>> 30 amber99_18 1 DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055
>> 31 amber99_44 1 DG5 O3' 31 -0.5232 16 ; qtot -0.2177
>> ....
>> .....
>>
>> My pdb file section:
>> ATOM 1 C5' DG5 A 1 28.937 -10.596 -28.986 1.00 95.46 C
>> ATOM 2 O5' DG5 A 1 30.060 -10.216 -29.774 1.00 95.82 O
>> ATOM 3 C4' DG5 A 1 29.239 -11.863 -28.212 1.00101.28 C
>> ATOM 4 O4' DG5 A 1 30.545 -11.736 -27.597 1.00102.88 O
>> ATOM 5 C3' DG5 A 1 28.300 -12.150 -27.052 1.00100.37 C
>> ATOM 6 O3' DG5 A 1 28.363 -13.527 -26.704 1.00104.13 O
>> ATOM 7 C2' DG5 A 1 28.913 -11.282 -25.960 1.00 95.28 C
>> ATOM 8 C1' DG5 A 1 30.395 -11.553 -26.200 1.00100.67 C
>> ATOM 9 N1 DG5 A 1 34.400 -10.292 -23.339 1.00 88.74 N
>> ATOM 10 C2 DG5 A 1 33.795 -11.515 -23.502 1.00 92.09 C
>> ATOM 11 N2 DG5 A 1 34.320 -12.542 -22.818 1.00 92.20 N
>> ATOM 12 N3 DG5 A 1 32.745 -11.722 -24.284 1.00100.66 N
>> ATOM 13 C4 DG5 A 1 32.342 -10.585 -24.901 1.00101.19 C
>> ATOM 14 C5 DG5 A 1 32.877 -9.321 -24.804 1.00 97.04 C
>> ATOM 15 C6 DG5 A 1 33.999 -9.114 -23.965 1.00 93.19 C
>> ATOM 16 O6 DG5 A 1 34.613 -8.059 -23.751 1.00 94.32 O
>> ATOM 17 N7 DG5 A 1 32.171 -8.426 -25.598 1.00 94.27 N
>> ATOM 18 C8 DG5 A 1 31.241 -9.155 -26.150 1.00 97.12 C
>> ATOM 19 N9 DG5 A 1 31.282 -10.474 -25.771 1.00100.33 N
>>
>> ....
>> .....
>>
>>
>> thanks
>> kamesh--
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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